vignettes/shinycsv-quickstart.Rmd
shinycsv-quickstart.RmdThis package has the code for a shiny application that allows you to interactively explore a table. The application allows you to subset or sort your data in different ways, explore one variable at a time, or make two-way plots. It also shows you the code to reproduce the figures and can handle many different types of tables thanks to (Neuwirth, 2022). The app also lets you choose which color to use in your plots.
You can view this shiny app deployed at libd.shinyapps.io/shinycsv. If you are interested in the showcase mode, then check out libd.shinyapps.io/shinycsv-showcase.
R is an open-source statistical environment which can be
easily modified to enhance its functionality via packages. shinycsv is
a R package available via GitHub. R can be
installed on any operating system from CRAN after which you can install
shinycsv by
using the following commands in your R session:
## If needed:
# install.packages('devtools')
library("devtools")
install_github("LieberInstitute/shinycsv")To use this package, simply run:
shinycsv::explore()The above command will open a shiny application where you can either
upload a CSV file
that has the variable names in the first column, a Rdata file
created with the save() function that has a single
data.frame object stored in it, an Excel file with a table in the first
sheet, or many other files as described at the rio
vignette. Using a Rdata file allows you to have stronger
control regarding the variable types (factor, date, etc) for each column
of your table.
As package developers, we try to explain clearly how to use our
packages and in which order to use the functions. But R has
a steep learning curve so it is critical to learn where to ask for help.
For shinycsv
please post issues in GitHub. However, please note that if you want to
receive help you should adhere to the posting
guidelines. It is particularly critical that you provide a small
reproducible example and your session information so package developers
can track down the source of the error.
We hope that shinycsv will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("shinycsv")## To cite package 'shinycsv' in publications use:
##
## Collado-Torres L, Semick S, Jaffe AE (2020). _shinycsv: Explore a
## table interactively in a shiny application_. R package version
## 0.99.9, <https://github.com/LieberInstitute/shinycsv>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {shinycsv: Explore a table interactively in a shiny application},
## author = {Leonardo Collado-Torres and Stephen Semick and Andrew E. Jaffe},
## year = {2020},
## note = {R package version 0.99.9},
## url = {https://github.com/LieberInstitute/shinycsv},
## }The shinycsv package (Wickham, 2011) was made possible thanks to:
Code for creating the vignette
## Create the vignette
library("rmarkdown")
system.time(render("shinycsv-quickstart.Rmd", "BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("shinycsv-quickstart.Rmd", tangle = TRUE)
## Clean up
file.remove("quickstartRef.bib")## [1] TRUEDate the vignette was generated.
## [1] "2023-05-07 07:21:17 UTC"Wallclock time spent generating the vignette.
## Time difference of 1.041 secsR session information.
## Loading required package: usethis## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.3.0 (2023-04-21)
## os Ubuntu 22.04.2 LTS
## system x86_64, linux-gnu
## ui X11
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## date 2023-05-07
## pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
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## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────This vignette was generated using BiocStyle (R Core Team, 2023) with knitr (Chang, Cheng, Allaire, Sievert et al., 2022) and rmarkdown (Oleś, 2023) running behind the scenes.
Citations made with knitcitations (Chan, Chan, Leeper, and Becker, 2021).
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